Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1235
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 34233
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Found at i:3929 original size:46 final size:46
Alignment explanation
Indices: 3857--3948 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
3847 CAGACTAAGC
*
3857 GCATTCGATACTGAGCACCAGAGGTACCTGTGGAAGAGGCCACGGT
1 GCATTCGATAATGAGCACCAGAGGTACCTGTGGAAGAGGCCACGGT
* * *
3903 GCATTCGATAATGAGCACCAGTGGTACTTGTGGAGGAGGCCACGGT
1 GCATTCGATAATGAGCACCAGAGGTACCTGTGGAAGAGGCCACGGT
3949 AGAGCTCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.25, C:0.22, G:0.34, T:0.20
Consensus pattern (46 bp):
GCATTCGATAATGAGCACCAGAGGTACCTGTGGAAGAGGCCACGGT
Found at i:9780 original size:27 final size:28
Alignment explanation
Indices: 9750--9927 Score: 152
Period size: 27 Copynumber: 6.5 Consensus size: 28
9740 ATATTGAGTC
* *
9750 CGCACACTCAGTGCTATATAAT-AAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
9777 CGCACACTTAGTGCTACGTAATCGAA-T
1 CGCACACTTAGTGCTACATAATCAAACT
*
9804 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
** ** * *
9832 CGCACACTTAGTGCCGCATGGTC-GATT
1 CGCACACTTAGTGCTACATAATCAAACT
* ***
9859 CGCACACTTAGTGC-ATCATATTC-GTTT
1 CGCACACTTAGTGCTA-CATAATCAAACT
* *
9886 CGCACACTTAGTGCAACATAGTCAAA-T
1 CGCACACTTAGTGCTACATAATCAAACT
9913 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9928 GTACAATTTA
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
27 102 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:9889 original size:82 final size:81
Alignment explanation
Indices: 9776--9926 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 81
9766 TATAATAAAC
* *
9776 TCGCACACTTAGTGCTACGTAATCGAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 TCGCACACTTAGTGCTACATAATCGAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
9841 AGTGCCGCATGGTCGAT
65 AGTGCCGCATGGTCGAT
* **
9858 TCGCACACTTAGTGC-ATCATATTCGTTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCTA-CATAATCGAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
9922 AGTGC
65 AGTGC
9927 TGTACAATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCTACATAATCGAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCGAT
Found at i:16302 original size:27 final size:27
Alignment explanation
Indices: 16272--16340 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
16262 ATATTGAGTC
* * *
16272 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
16299 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
16326 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16341 GTACAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:16353 original size:27 final size:26
Alignment explanation
Indices: 16272--16353 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 26
16262 ATATTGAGTC
* * * *
16272 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCT-TACAATTAAAT
*
16299 CGCACACTTAGTGC-TACGTAATCAAAT
1 CGCACACTTAGTGCTTAC--AATTAAAT
*
16326 CGCACACTTAGTGCTGTACAATTTAAT
1 CGCACACTTAGTGCT-TACAATTAAAT
16353 C
1 C
16354 CCGCGCACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
25 2 0.04
27 41 0.89
29 3 0.07
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (26 bp):
CGCACACTTAGTGCTTACAATTAAAT
Found at i:21055 original size:12 final size:11
Alignment explanation
Indices: 21029--21060 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
21019 AATACACCCT
21029 AGAAGAGGAGA
1 AGAAGAGGAGA
21040 AGAAGAGGACGA
1 AGAAGAGGA-GA
21052 AGAAGAGGA
1 AGAAGAGGA
21061 AGCAAGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.53, C:0.03, G:0.44, T:0.00
Consensus pattern (11 bp):
AGAAGAGGAGA
Found at i:23696 original size:27 final size:27
Alignment explanation
Indices: 23665--23842 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
23655 TAAATTGTAC
23665 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
23692 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
23718 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
23746 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
23774 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
23801 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
23828 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
23843 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:23779 original size:82 final size:81
Alignment explanation
Indices: 23666--23821 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
23656 AAATTGTACA
* *
23666 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
23730 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
23747 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
23812 TGCGAGTTGA
65 TGCGAATTGA
23822 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:23833 original size:82 final size:81
Alignment explanation
Indices: 23662--23842 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
23652 GATTAAATTG
* *
23662 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
23727 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
23743 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
23807 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
23825 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
23843 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31762 original size:27 final size:27
Alignment explanation
Indices: 31731--31908 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31721 TAAATTGTAC
31731 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31758 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31784 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31812 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31840 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31867 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31894 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31909 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31845 original size:82 final size:81
Alignment explanation
Indices: 31732--31887 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31722 AAATTGTACA
* *
31732 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31796 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31813 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31878 TGCGAGTTGA
65 TGCGAATTGA
31888 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31899 original size:82 final size:81
Alignment explanation
Indices: 31728--31908 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
31718 GATTAAATTG
* *
31728 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31793 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31809 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31873 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31891 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31909 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.